ORCID Profile
0000-0002-8274-6265
Current Organisations
University of Western Australia
,
Telethon Kids Institute
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Publisher: Cold Spring Harbor Laboratory
Date: 02-07-2022
DOI: 10.1101/2022.07.01.22277170
Abstract: Pneumonia remains a leading cause of hospitalization and death among young children worldwide, and the diagnostic challenge of differentiating bacterial from non-bacterial pneumonia is the main driver of antibiotic use for treating pneumonia in children. Causal Bayesian networks (BNs) serve as powerful tools for this problem as they provide clear maps of probabilistic relationships between variables and produce results in an explainable way by incoporating both domain expert knowledge and numerical data. We used domain expert knowledge and data in combination and iteratively, to construct, parameterise and validate a causal BN to predict causative pathogens for childhood pneumonia. Expert knowledge elicitation occurred through a series of group workshops, surveys and one-on-one meetings involving 6-8 experts from erse domain areas. The model performance was evaluated based on both quantitative metrics (area under the receiver-operator curve (AUROC) and log loss) and qualitative expert validation. Sensitivity analyses were conducted to investigate how the target output is influenced by varying key assumptions of particular high degree of uncertainty around data or domain expert knowledge. Designed to apply to a cohort of children with X-ray confirmed pneumonia who presented to a tertiary paediatric hospital in Australia, the resulting BN offers explainable and quantitative predictions on a range of variables of interest, including the diagnosis of bacterial pneumonia, detection of respiratory pathogens in the nasopharynx, and the clinical phenotype of a pneumonia episode. Satisfactory numeric performance has been achieved including an AUROC of 0.8 in predicting the clinical diagnosis of bacterial pneumonia. Three commonly encountered scenarios were presented to demonstrate the potential usefulness of the BN outputs in various clinical pictures. To our knowledge, this is the first causal model developed to help determine the causative pathogen for paediatric pneumonia. It can be utilized to derive recommendations to support more directed and judicious use of antimicrobials for relevant cohorts. The BN needs further validation before it can be clinically implemented. Our model framework and the methodological approach can be adapted beyond our context to broad respiratory infections and geographical and healthcare settings.
Publisher: JMIR Publications Inc.
Date: 17-01-2022
DOI: 10.2196/29889
Abstract: Acute respiratory infection (ARI) in childhood is common, but more knowledge on the burden and natural history of ARI in the community is required. A better understanding of ARI risk factors, treatment, and outcomes will help support parents to manage their sick child at home. Digital health tools are becoming more widely adopted in clinical care and research and may assist in understanding and managing common pediatric diseases, including ARI, in hospitals and in the community. We integrated 2 digital tools—a web-based discharge communication system and the REDCap (Research Electronic Data Capture) platform—into the Pragmatic Adaptive Trial for Acute Respiratory Infection in Children to enhance parent and physician engagement around ARI discharge communication and our patient registry. The objective of this study is to determine the efficacy and usability of digital tools integrated into a pediatric patient registry for ARI. Semistructured interviews and software interface usability testing were conducted with 11 parents and 8 emergency department physicians working at a tertiary pediatric hospital and research center in Perth, Western Australia, in 2019. Questions focused on experiences of discharge communication and clinical trial engagement. Responses were analyzed using the qualitative Framework Method. Participants were directly observed using digital interfaces as they attempted predetermined tasks that were then classified as success, failure, software failure, or not observed. Participants rated the interfaces using the System Usability Scale (SUS). Most parents (9/11, 82%) indicated that they usually received verbal discharge advice, with some (5/11, 45%) recalling receiving preprinted resources from their physician. Most (8/11, 73%) would also like to receive discharge advice electronically. Most of the physicians (7/8, 88%) described their usual practice as verbal discharge instructions, with some (3/8, 38%) reporting time pressures associated with providing discharge instructions. The digital technology option was preferred for engaging in research by most parents (8/11, 73%). For the discharge communication digital tool, parents gave a mean SUS score of 94/100 (SD 4.3 A grade) for the mobile interface and physicians gave a mean usability score of 93/100 (SD 4.7 A grade) for the desktop interface. For the research data management tool (REDCap), parents gave a mean usability score of 78/100 (SD 11.0 C grade) for the mobile interface. Semistructured interviews allowed us to better understand parent and physician experiences of discharge communication and clinical research engagement. Software interface usability testing methods and use of the SUS helped us gauge the efficacy of our digital tools with both parent and physician users. This study demonstrates the feasibility of combining qualitative research methods with software industry interface usability testing methods to help determine the efficacy of digital tools in a pediatric clinical research setting.
Publisher: BMJ
Date: 07-2020
DOI: 10.1136/BMJRESP-2020-000593
Abstract: Detection of pneumonia-causing respiratory viruses in the nasopharynx of asymptomatic children has made their actual contribution to pneumonia unclear. We compared nasopharyngeal viral density between children with and without pneumonia to understand if viral density could be used to diagnose pneumonia. Nasopharyngeal swabs (NPS) were collected from hospitalised pneumonia cases at Princess Margaret Hospital (PMH) and contemporaneous age-matched controls at PMH outpatient clinics and a local immunisation clinic in Perth, Australia. The density (copies/mL) of respiratory syncytial virus (RSV), influenza A virus (InfA), human metapneumovirus (HMPV) and rhinovirus in NPS was determined using quantitative PCR. Linear regression analysis was done to assess the trend between viral density and age in months. The association between viral density and disease status was examined using logistic regression. Area under receiver operating characteristic (AUROC) curves were assessed to determine optimal discriminatory viral density cut-offs. Through May 2015 to October 2017, 230 pneumonia cases and 230 controls were enrolled. Median nasopharyngeal density for any respiratory virus was not substantially higher in cases than controls (p .05 for each). A decreasing density trend with increasing age was observed—the trend was statistically significant for RSV (regression coefficient −0.04, p=0.004) but not for other viruses. After adjusting for demographics and other viral densities, for every log 10 copies/mL density increase, the odds of being a case increased by six times for RSV, three times for HMPV and two times for InfA. The AUROC curves were .70 for each virus, suggesting poor case–control discrimination based on viral density. The nasopharyngeal density of respiratory viruses was not significantly higher in children with pneumonia than those without however, the odds of being a case increased with increased density for some viruses. The utility of viral density, alone, in defining pneumonia was limited.
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 2018
Publisher: BMJ
Date: 27-01-2021
DOI: 10.1136/THORAXJNL-2020-216032
Abstract: Empyema is a serious complication of pneumonia frequently caused by Streptococcus pneumoniae (SP). We assessed the impact of the 13-valent pneumococcal conjugate vaccine (13vPCV) on childhood pneumonia and empyema after inclusion in the Australian National Immunisation Program. For bacterial pneumonia and empyema hospitalisations, we ascertained incidence rates (IRs) using the National Hospital Morbidity Database International Statistical Classification of Disease discharge codes and relevant population denominators, and calculated incidence rate ratios (IRR) comparing the 13vPCV period (June 2012–May 2017) with the 7vPCV period (June 2007–May 2011). Blood and pleural fluid (PF) cultures and PF PCR of 401 children with empyema from 11 Australian hospitals during the 13vPCV period were compared with our previous study in the 7vPCV period. Across 7vPCV and 13vPCV periods, IRs per million children (95% CIs) were 1605 (1588 to 1621) and 1272 (1259 to 1285) for bacterial pneumonia, and 14.23 (12.67 to 15.79) and 17.89 (16.37 to 19.42) for empyema hospitalisations. IRRs were 0.79 (0.78 to 0.80) for bacterial pneumonia and 1.25 (1.09 to 1.44) for empyema. Of 161 empyema cases with SP serotypes, 147 (91.3%) were vaccine types. ST3 accounted for 76.4% of identified serotypes in the 13vPCV period, more than double than the 7vPCV period (p .001) ST19A decreased from 36.4% to 12.4%. No cases of ST1 empyema were identified in the 13vPCV period versus 14.5% in the 7vPCV period. 13vPCV resulted in a significant reduction in all-cause hospitalisations for bacterial pneumonia but empyema hospitalisations significantly increased, with emergence of pneumococcal ST3 as the dominant serotype in empyema. Australian and New Zealand Clinical Trial Registry ACTRN 12614000354684.
Publisher: American Society of Tropical Medicine and Hygiene
Date: 02-07-2014
Publisher: American Academy of Pediatrics (AAP)
Date: 03-2021
Abstract: Children with medical comorbidities are at greater risk for severe influenza and poorer clinical outcomes. Despite recommendations and funding, influenza vaccine coverage remains inadequate in these children. We aimed to systematically review literature assessing interventions targeting influenza vaccine coverage in children with comorbidities and assess the impact on influenza vaccine coverage. PubMed, Scopus, Embase, Cumulative Index to Nursing and Allied Health Literature, Cochrane Central Register of Controlled Trials, Allied and Complementary Medicine Database, and Web of Science databases were searched. Interventions targeting influenza vaccine coverage in children with medical comorbidities. Two reviewers independently screened articles, extracting studies’ methods, interventions, settings, populations, and results. Four reviewers independently assessed risk of bias. From 961 screened articles, 35 met inclusion criteria. Published studies revealed that influenza vaccine coverage was significantly improved through vaccination reminders and education directed at either patients’ parents or providers, as well as by vaccination-related clinic process changes. Interventions improved influenza vaccine coverage by an average 60%, but no significant differences between intervention types were detected. Significant bias and study heterogeneity were also identified, limiting confidence in this effect estimate. A high risk of bias and overall low quality of evidence limited our capacity to assess intervention types and methods. Interventions were shown to consistently improve influenza vaccine coverage however, no significant differences in coverage between different intervention types were observed. Future well-designed studies evaluating the effectiveness of different intervention are required to inform future optimal interventions.
Publisher: MDPI AG
Date: 31-01-2019
Abstract: Otitis media (OM) is a major reason for antibiotic consumption and surgery in children. Nasopharyngeal carriage of otopathogens, Streptococcus pneumoniae and nontypeable Haemophilus influenzae (NTHi), is a prerequisite for development of OM, and increased nasopharyngeal otopathogen density correlates with disease onset. Vaccines can reduce or eliminate otopathogen carriage, as demonstrated for pneumococcal serotypes included in pneumococcal conjugate vaccines (PCV). The 10-valent PCV (PCV10) includes an NTHi carrier protein, and in 2011 superseded 7-valent PCV on the New Zealand Immunisation Program. Data are conflicting on whether PCV10 provides protection against NTHi carriage or disease. Assessing this in otitis-prone cohorts is important for OM prevention. We compared otopathogen density in the nasopharynx and middle ear of New Zealand PCV7-vaccinated and PCV10-vaccinated otitis-prone and non-otitis-prone children to determine PCV10 impact on NTHi and S. pneumoniae carriage. We applied qPCR to specimens collected from 217 PCV7-vaccinated children (147 otitis-prone and 70 non-otitis-prone) and 240 PCV10-vaccinated children (178 otitis-prone and 62 non-otitis-prone). After correcting for age and day-care attendance, no difference was observed between NTHi density in the nasopharynx of PCV7-vaccinated versus PCV10-vaccinated otitis-prone (p = 0.563) or non-otitis-prone (p = 0.513) children. In contrast, pneumococcal nasopharyngeal density was higher in PCV10-vaccinated otitis-prone children than PCV7-vaccinated otitis-prone children (p = 0.003). There was no difference in otopathogen density in middle ear effusion from PCV7-vaccinated versus PCV10-vaccinated otitis-prone children (NTHi p = 0.918 S. pneumoniae p = 0.415). When pneumococcal carriage was assessed by vaccine serotypes (VT) and non-vaccine serotypes (NVT), there was no difference in VT density (p = 0.546) or NVT density (p = 0.315) between all PCV7-vaccinated versus all PCV10-vaccinated children. In summary, PCV10 did not reduce NTHi density in the nasopharynx or middle ear, and was associated with increased pneumococcal nasopharyngeal density in otitis-prone children in New Zealand. Development of therapies that prevent or reduce otopathogen colonisation density in the nasopharynx are warranted to reduce the burden of OM.
Publisher: Public Library of Science (PLoS)
Date: 28-10-2019
Publisher: BMJ
Date: 18-10-2019
DOI: 10.1136/THORAXJNL-2018-212096
Abstract: Respiratory pathogens associated with childhood pneumonia are often detected in the upper respiratory tract of healthy children, making their contribution to pneumonia difficult to determine. We aimed to determine the contribution of common pathogens to pneumonia adjusting for rates of asymptomatic detection to inform future diagnosis, treatment and preventive strategies. A case–control study was conducted among children years in Perth, Western Australia. Cases were children hospitalised with radiologically confirmed pneumonia controls were healthy children identified from outpatient and local immunisation clinics. Nasopharyngeal swabs were collected and tested for 14 respiratory viruses and 6 bacterial species by Polymerase chain reaction (PCR). For each pathogen, adjusted odds ratio (aOR 95% CI) was calculated using multivariate logistic regression and population-attributable fraction (95% CI) for pneumonia was estimated. From May 2015 to October 2017, 230 cases and 230 controls were enrolled. At least one respiratory virus was identified in 57% of cases and 29% of controls (aOR: 4.7 95% CI: 2.8 to 7.8). At least one bacterial species was detected in 72% of cases and 80% of controls (aOR: 0.7 95% CI: 0.4 to 1.2). Respiratory syncytial virus (RSV) detection was most strongly associated with pneumonia (aOR: 58.4 95% CI: 15.6 to 217.5). Mycoplasma pneumoniae was the only bacteria associated with pneumonia (aOR: 14.5 95% CI: 2.2 to 94.8). We estimated that RSV, human metapneumovirus (HMPV), influenza, adenovirus and Mycoplasma pneumoniae were responsible for 20.2% (95% CI: 14.6 to 25.5), 9.8% (5.6% to 13.7%), 6.2% (2.5% to 9.7%), 4% (1.1% to 7.1%) and 7.2% (3.5% to 10.8%) of hospitalisations for childhood pneumonia, respectively. Respiratory viruses, particularly RSV and HMPV, are major contributors to pneumonia in Australian children.
Publisher: Oxford University Press (OUP)
Date: 24-07-2012
Abstract: Although influenza is a vaccine-preventable disease that annually causes substantial disease burden, data on virus activity in tropical countries are limited. We analyzed publicly available influenza data to better understand the global circulation of influenza viruses. We reviewed open-source, laboratory-confirmed influenza surveillance data. For each country, we abstracted data on the percentage of s les testing positive for influenza each epidemiologic week from the annual number of s les testing positive for influenza. The start of influenza season was defined as the first week when the proportion of s les that tested positive remained above the annual mean. We assessed the relationship between percentage of s les testing positive and mean monthly temperature with use of regression models. We identified data on laboratory-confirmed influenza virus infection from 85 countries. More than one influenza epidemic period per year was more common in tropical countries (41%) than in temperate countries (15%). Year-round activity (ie, influenza virus identified each week having ≥ 10 specimens submitted) occurred in 3 (7%) of 43 temperate, 1 (17%) of 6 subtropical, and 11 (37%) of 30 tropical countries with available data (P = .006). Percentage positivity was associated with low temperature (P = .001). Annual influenza epidemics occur in consistent temporal patterns depending on climate.
Publisher: International Global Health Society
Date: 15-03-2016
Publisher: Public Library of Science (PLoS)
Date: 25-02-2014
Publisher: Springer Science and Business Media LLC
Date: 31-08-2018
Publisher: BMJ
Date: 03-2018
DOI: 10.1136/BMJOPEN-2017-020646
Abstract: Pneumonia is the leading cause of childhood morbidity and mortality globally. Introduction of the conjugate Haemophilus influenzae B and multivalent pneumococcal vaccines in developed countries including Australia has significantly reduced the overall burden of bacterial pneumonia. With the availability of molecular diagnostics, viruses are frequently detected in children with pneumonia either as primary pathogens or predispose to secondary bacterial infection. Many respiratory pathogens that are known to cause pneumonia are also identified in asymptomatic children, so the true contribution of these pathogens to childhood community-acquired pneumonia (CAP) remains unclear. Since the introduction of pneumococcal vaccines, very few comprehensive studies from developed countries have attempted to determine the bacterial and viral aetiology of pneumonia. We aim to determine the contribution of bacteria and viruses to childhood CAP to inform further development of effective diagnosis, treatment and preventive strategies. We are conducting a prospective case–control study (PneumoWA) where cases are children with radiologically confirmed pneumonia admitted to Princess Margaret Hospital for Children (PMH) and controls are healthy children identified from PMH outpatient clinics and from local community immunisation clinics. The case–control ratio is 1:1 with 250 children to be recruited in each arm. Nasopharyngeal swabs are collected from both cases and controls to detect the presence of viruses and bacteria by PCR pathogen load will be assessed by quantitative PCR. The prevalence of pathogens detected in cases and controls will be compared, the OR of detection and population attributable fraction to CAP for each pathogen will be determined relationships between pathogen load and disease status and severity will be explored. This study has been approved by the human research ethics committees of PMH, Perth, Australia (PMH HREC REF 2014117EP). Findings will be disseminated at research conferences and in peer-reviewed journals.
Publisher: JMIR Publications Inc.
Date: 25-04-2021
Abstract: cute respiratory infection (ARI) in childhood is common, but more knowledge on the burden and natural history of ARI in the community is required. A better understanding of ARI risk factors, treatment, and outcomes will help support parents to manage their sick child at home. Digital health tools are becoming more widely adopted in clinical care and research and may assist in understanding and managing common pediatric diseases, including ARI, in hospitals and in the community. We integrated 2 digital tools—a web-based discharge communication system and the REDCap (Research Electronic Data Capture) platform—into the Pragmatic Adaptive Trial for Acute Respiratory Infection in Children to enhance parent and physician engagement around ARI discharge communication and our patient registry. he objective of this study is to determine the efficacy and usability of digital tools integrated into a pediatric patient registry for ARI. emistructured interviews and software interface usability testing were conducted with 11 parents and 8 emergency department physicians working at a tertiary pediatric hospital and research center in Perth, Western Australia, in 2019. Questions focused on experiences of discharge communication and clinical trial engagement. Responses were analyzed using the qualitative Framework Method. Participants were directly observed using digital interfaces as they attempted predetermined tasks that were then classified as i success /i , i failure /i , i software failure /i , or i not observed /i . Participants rated the interfaces using the System Usability Scale (SUS). ost parents (9/11, 82%) indicated that they usually received verbal discharge advice, with some (5/11, 45%) recalling receiving preprinted resources from their physician. Most (8/11, 73%) would also like to receive discharge advice electronically. Most of the physicians (7/8, 88%) described their usual practice as verbal discharge instructions, with some (3/8, 38%) reporting time pressures associated with providing discharge instructions. The digital technology option was preferred for engaging in research by most parents (8/11, 73%). For the discharge communication digital tool, parents gave a mean SUS score of 94/100 (SD 4.3 A grade) for the mobile interface and physicians gave a mean usability score of 93/100 (SD 4.7 A grade) for the desktop interface. For the research data management tool (REDCap), parents gave a mean usability score of 78/100 (SD 11.0 C grade) for the mobile interface. emistructured interviews allowed us to better understand parent and physician experiences of discharge communication and clinical research engagement. Software interface usability testing methods and use of the SUS helped us gauge the efficacy of our digital tools with both parent and physician users. This study demonstrates the feasibility of combining qualitative research methods with software industry interface usability testing methods to help determine the efficacy of digital tools in a pediatric clinical research setting.
Publisher: Informa UK Limited
Date: 03-2017
DOI: 10.2147/PPA.S121800
Publisher: Wiley
Date: 22-04-2014
DOI: 10.1111/IRV.12254
Publisher: Springer Science and Business Media LLC
Date: 08-05-2013
Publisher: Elsevier BV
Date: 2021
Publisher: American Society of Tropical Medicine and Hygiene
Date: 08-2011
Publisher: Springer Science and Business Media LLC
Date: 02-04-2019
Publisher: International Global Health Society
Date: 07-03-2017
Publisher: SAGE Publications
Date: 08-2012
Abstract: A cross-sectional study was conducted among youth clients of hotel-based female sex workers (YCHBFSWs) in nine randomly selected hotels in Bangladesh to examine sexual-risk behaviour, condom use and determinants of condom use in last sex, knowledge of HIV, sexually transmitted infection (STI) prevalence and STI care-seeking behaviour. A prestructured questionnaire was used to collect sociodemographic, behavioural, clinical information urine specimens (before sex) and blood were collected for diagnosis of Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, syphilis and herpes simplex virus 2 (HSV2) infection. One thousand and thirteen participants were enroled in the study. Approximately half of them reported visiting female sex workers (FSWs) at least once a month and 25% visited FSWs at least once a week. Only 12% of participants reported regular condom use. The prevalence of N. gonorrhoeae, C. trachomatis, T. vaginalis, syphilis and HSV2 was 2.2%, 3.9%, 7.2%, 2.6% and 12.9%, respectively. Only 15.3% of the YCHBFSW sought STI care in the past year. Negotiation of condom use with FSWs was the main determinant (odds ratio = 17.95) for condom use at last sex. Male clients of FSWs, including YCHBFSW, are an important bridge population for HIV transmission in Bangladesh and HIV interventions should be designed and implemented for them.
Location: Bangladesh
Location: Bangladesh
Start Date: 2020
End Date: 2018
Funder: Merck
View Funded ActivityStart Date: 2017
End Date: 2018
Funder: Princess Margaret Hospital Foundation
View Funded Activity